Genome-Resolved Metagenomics Analysis of Rice Straw Degradation Experiments Unveils MAGs with High Potential to Decompose Lignocellulosic Residues

Jeferyd Yepes-Garcíaa, Nicolás Novoa-Montenegro, Vanessa Otero-Jiménez, Daniel Uribe-Vélez, Emiliano Barreto-Hernández, Laurent Falquet

December, 2024

Department of Biology, University of Fribourg, Fribourg, Canton of Fribourg, 1700, Switzerland

Swiss Institute of Bioinformatics, Lausanne, Vaud, 1015, Switzerland

Agricultural Microbiology Group, Biotechnology Institute, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C., Colombia

Department of Soil and Water Systems, University of Idaho, 875 Perimeter Drive MS2340, Moscow, ID 83844-2340, United States of America

Bioinformatics group, Biotechnology Institute, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C., Colombia

Correspondence should be addressed to L.F ()

Abstract

Background Rice is one of the top three crops that contribute 60% of the calories consumed by humans worldwide. Nonetheless, extensive rice harvesting yields more than 800 tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. As a result, millions of tons of carbon dioxide and greenhouse gases are released, causing issues such as respiratory problems, soil degradation and global warming. In this work, we explore the biological decomposition of RS through the application of microbial consortia from a metagenomics perspective.

Results We applied different treatments to RS placed in a mulching setup during experiments carried out in Colombian rice fields, using various combinations of a Trichoderma-based commercial product, the bacterial strain Bacillus altitudinis, organic nitrogen, and a mixture of potassium-reducing organic acids. Before inoculation and after 30 days of treatment, we characterized the microbial community on the surface of the material and from the bulk soil by performing a reference-based compositional analysis, and reconstructing and functionally annotating Metagenome-Assembled Genomes (MAGs). High-quality MAGs with great potential to decompose RS, represented by the extensive number of carbohydrate-active enzymes, were recovered. Soil MAGs taxonomic classification indicates that they may represent potential novel microbial taxa, while the main part of the RS MAGs with superior lignocellulose-degrading capacity were affiliated under Actinomycetota and Bacteroidota phyla. Moreover, the biotransformation capacity of the MAGs was indirectly verified by quantifying β-glucosidase activity of the samples they were extracted from, and an improvement on the action of this enzyme was detected, suggesting cellulose degradation by the native microbiota possibly triggered by Trichoderma sp.

Conclusions This contribution underscores the possibility of promoting RS degradation through biological strategies by the activation of native microorganisms. Further, the newly unveiled MAGs with high RS-degrading potential provide a valuable resource for exploring the functional potential of previously uncharacterized microbial diversity in Colombian agricultural ecosystems, including microorganisms that have not been previously reported as remarkable lignocellulose decomposers.

Graphical Abstract

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Methodology

Reference-based compositional analysis

We used Kraken2/Bracken to perform taxonomic assignment of the reads. The procedure included the remotion of reads mapping the rice genome (O. zativa, RefSeq accession number: GCF_000005425.2). The workflow is proposed by Lu et al. (2022), wrapped by Nextflow.

The analysis of the raw counts was developed by wrapping the output as a Phyloseq object to estimate effect of treatments and time over relative abundance, α-Diversity, β-Diversity and differentially abundant taxa.

MAG recovery

nf-core/mag was implemented to build and annotate the MAGs from the raw sequences. A co-assembly/co-binning strategy was chosen as an attempt to improve the quality and resolution of the MAGs. MEGAHIT was used for the assembly, while MaxBin2 and MetaBAT2 were the selected tools for binning. A de-replication and refinement step was carried by enabling DASTool within the workflow. For the downstream analysis, the curated MAGs were analyzed with MAGFlow/BIgMAG, that includes quality-measuring tools such as CheckM2, BUSCO, GUNC and QUAST, as well as the taxonomic annotator GTDB-Tk2 relying on the database version R220. The presence of carbohydrate-related metabolism enzymes was studied through dbCAN3 along with the CAZy database, whilst Cluster of Orthologous Genes (COGs) were detected by COGclassifier. The selection of the MAGs was carried out using the criteria: completeness above 50% and contamination below 10%. In addition, MAGS belonging to either rice straw or soil with average differences <5% ANI were clustered using FastANI. For data visualization, Circos, iTOL and ggplot2 packages were used.

Fig. 1. Bioinformatics workflow followed to evaluate sequence quality, perform reference-based compositional analysis, and MAG recovery.

Results

MAGs and CAZyme information

Fig. 2. a Two-dimensional Uniform Manifold Approximation and Projection (UMAP) embedding of normalized CAZy enzymes counts per MAG (before clustering with FastANI) colored by phylum (GTDB-Tk2). All CAZy classes (GH, GT, PL, CE, AA and CBMs), along with all their families, were considered for clustering using default values (15 neighbors and Euclidean distance). b Taxonomic classification (at the domain and phylum levels), quality (CheckM2), and identification as species or not of the clustered MAGs from the RS and soil metagenomes. The exact order of the missing phylum labels within the b plot can be read from the legend on a.

Fig. 3. Recovered MAGs from RS samples after clustering based on Average Nucleotide Identity (ANI). The visualization includes phylogenetic relationship among them (tree), specific highlighted phylum clades (colored sectors), genus classification (outer text), proportion of the main categories of Cluster of Orthologous Genes (COG) within each MAG (blue-orange-red-green pie chart), Carbon Active EnZyme (CAZyme) class normalized abundance (red scaled heatmap), classification as either high-quality or mid-quality MAG based on checkM2 measurements (blue binary), GUNC test passing (green binary), and genome size in Mbp (outer black bars).The displayed MAGs are representatives from the generated clusters using ANI, and they were selected based on the score: completeness – 0.5 x contamination. Conventions in CAZyme heatmap: GH glycoside hydrolases, GT glyco-syltransferases, PL polysaccharide lyases, CE carbohydrate esterases, CBMs carbohydrate-binding modules, AA auxiliary activities.

Fig. 4. Recovered MAGs from soil samples after clustering based on Average Nucleotide Identity (ANI). See Fig. 3 for feature explanation.

Fig. 5. Bubble plot depicting the number of normalized counts for CAZyme families associated with lignocellulose-degrading enzymes found in the MAGs recovered from RS samples. Visualization includes: MAG clustering based on normalized CAZyme counts of the selected families, and phylum information (GTDB-Tk2). The classification as MQ MAG or HQ MAG (CheckM2) is designated by the shape in the bubble plot. The displayed MAGs are representatives from the generated clusters using ANI, and they were selected based on the score: completeness – 0.5 x contamination. Displayed RS MAGs contain at least 30 normalized counts in 5 or more CAZyme families; complete information about normalized CAZyme counts in RS MAGs is found in Fig. S15.

Fig. 6. Bubble plot depicting the number of normalized counts for CAZyme families associated with lignocellulose-degrading enzymes found in the clustered MAGs recovered from soil samples. See Fig. 5 for feature explanation. All soil MAGs are displayed.

Fig. 7. Boxplot showing the distribution and abundance of normalized counts for CAZyme families associated with lignocellulose-degrading enzymes found in the MAGs recovered from RS and soil samples.

β‑Glucosidase activity

Fig. 8. Left: bubble plot depicting normalized CAZyme counts for β-glucosidase families (GH1, GH3, GH5 and GH9) per sample; GH glycoside hydrolases. Right: data distribution of experimental β-glucosidase activity per sample. The displayed normalized CAZyme values represent the maximum count in a given MAG of each GH family within the sample; treatment colors are shared by both the bubble plot and the boxplot.

Supplementary Figures

Field experiments

Fig. S1. Field diagram of plots and yard distribution, illustrating yard sizing and color plotting distribution on the field. Green dot lines indicate rice furrows without treatment used as a natural barrier between plot treatments. Blank spots represent spaces without treatments due to field irregular terrain impeding a treatment application. Arrow indicates magnetic north.

Fig. S2. Illustration of sampling points for soil and straw for physicochemical and enzymatic analysis on field. A shows the distribution of soil sampling points within each plot; B depicts the distribution of rice straw sampling points within each plot; C displays a field picture showing the marks used for the replicas and color code per treatment: pink represents Cont plots, blue FBa plots, yellow FBaNit plots, and violet FCent plots; D presents RS manual collection; E exemplifies a tube probe for soil sampling; and F,G exhibit soil sample disposal in marked Ziploc® bags.

Soil parameters

Fig. S3. Experimental measures of physicochemical parameters in soil samples including total carbon, total nitrogen, pH and phosphorus. The data were normalized using the Min-Max method to adjust the raw values to the same scale; the displayed numbers represent the mean of the quantified parameter per sample.

Enzymatic activity

Fig. S4. Experimental protease, acid, and alkaline phosphatase activities of rice straw (a) and soil (b) samples. The enzymatic activity was measured according to the guidelines established by Alef & Nannipieri (1995).

Reference-based analysis

Fig. S5. Screenshot of a Krona plot displaying the taxonomic classification and relative abundance, performed with Kraken2 coupled to Bracken, of the reads belonging to the mock community sequenced as part of quality control for the DNA extraction process.

Fig. S6. Taxonomic profiling of the sequences using Kraken2 coupled to Bracken: a Relative domain abundance per matrix source, merging all the replicates per sample. b α-Diversity, colored by treatment, measured through Shannon and Inverse Simpson indices. c Sample ordination through Principal Coordinate Analysis (PCoA) using a Bray-Curtis dissimilarity matrix as input. The ellipses represent 95% confidence regions around the centroids of each group calculated by the assumption of multivariate t-distribution. d Two-dimensional Uniform Manifold Approximation and Projection (UMAP) embedding of β-Diversity estimation of the samples based on the Aitchison distance. e Compositional variability of the samples, measured as distance to the centroid in a multivariate space computed with the Aitchison distance among samples. ANOVA analysis results show no significant differences in terms of group dispersion. f Proportion of the variance explained by the factors Time and Treatment, segmented by matrix source, in Permutational Analysis of Variance (PERMANOVA) implemented according to different distance/dissimilarity metrics; the significance of each factor is determined by the symbol color. g Selected differentially abundant genera in RS samples based on Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2). Left: log2FC of treatments to Cont0, and Right: Boxplots of selected genera abundance (counts) in log10 scale. All displayed genera exhibit p-value < 0.05 adjusted with Holm–Bonferroni method for multiple comparisons. Cont0 and Cont1 in RS comparisons indicate Cont samples at time 0 and 1, respectively. Differences throughout time for all treatments against Cont samples at time 0 are shown. All the analysis from b to f were carried out only with Bacteria data and normalized counts as Counts per million (CPM). The treatment colors are transversal to plots b, c, d, e, f and g. ANCOM-BC2 was implemented with agglomerated data at genus level, and with the most abundant taxa (> 0.5%).

Fig. S7. Percentage of annotated reads using Kraken2/Bracken segmented by matrix and time point. For rice straw at time 0 samples were taken from a bulk of material; this same bulk was subsampled with specific amounts of rice straw to start the experiments, and hence accounting with only 1 sample at time 0.

Fig. S8. Relative phylum (a, c) and genus (b, d) abundance of agglomerated data (Bacteria, top; Eukaryota, bottom). Displaying abundance values that belong to the portion of the reads annotated in each domain (see Fig. S6a and Fig. S7). Replicates were merged, and the panels are split by matrix source. On phylum plots, only phyla with relative abundance above 0.5% are displayed, whilst on genus plots genera above 3% and 2% are depicted for Bacteria and Eukaryota, respectively.

Fig. S9. Relative genus abundance of agglomerated RS data with panels split by treatment. Only genera with relative abundance above 3% are displayed.

MAG reconstruction

Fig. S10. Metrics summaries of the MAGs built from RS (a) and soil (b) samples; the columns represent, in order, the proportion of: mid-quality and high-quality MAGs according to CheckM2 estimations; MAGs passing the GUNC test; and annotated MAGs at different taxonomic levels based on GTDB-Tk2.

Fig. S11. Presence/absence of MAGs annotated with GTDB-Tk2 in RS samples at genus level. Genome size, in Mbp, is indicated as the point size, while the color scale represents the relative abundance of each MAG per sample, and the point shape shows whether the displayed MAG is classified as high-quality or mid-quality (CheckM2). When MAGs with the same genus annotation were found in the same sample, the most complete one is depicted and their abundances are added up.

Fig. S12. Presence/absence of MAGs annotated with GTDB-Tk2 in soil samples at genus level. Genome size, in Mbp, is indicated as the point size, while the color scale represents the relative abundance of each MAG per sample, and the point shape shows whether the displayed MAG is classified as high-quality or mid-quality (CheckM2). When MAGs with the same genus annotation were found in the same sample, the most complete one is depicted and their abundances are added up.

MAGs and CAZyme information

Fig. S13. Circos plots showing the proportion of the 4 main categories (Metabolism; Information Storage and Processing; Cellular Processes and Signaling; and Protein Coding Sequences with Unknown function) of Clusters of Orthologous Genes (COGs) found within the MAGs recovered from RS (top) and soil (bottom) the samples. The inner ring accounts for the total number of COGs related to every sample or COG category; the outer ring depicts the relative abundance of COGs from each sample or COG category; the width of the ribbons linking any sample and a COG category depicts their relative abundance to each other. The number of counts per category was normalized using the total number of genes found per MAG.

Fig. S14. Two-dimensional Uniform Manifold Approximation and Projection (UMAP) embedding of normalized CAZy enzymes counts per MAG (before clustering with FastANI) colored by treatment and shape by the time in which the MAGs were recovered.

Fig. S15. Clustered MAGs recovered from **RS* samples and their normalized counts for CAZy families associated with lignocellulose-degrading enzymes.The organization of the tree relies on the phylogenetic information retrieved from GTDB-Tk2. The displayed MAGs are representatives from the generated clusters using ANI, and they were selected based on the following score: completeness – 0.5 x contamination.

Supplementary Tables

GTDB taxonomy of RS MAGs

Bin Treatment Matrix Time MAG Domain Phylum Class Order Family Genus Species
ContRs0_10 Cont Rice straw 0 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Thermomonas Unclassified
ContRs0_11 Cont Rice straw 0 Mid-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium sp002500745
ContRs0_12 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Streptomycetales Streptomycetaceae Streptomyces Streptomyces bacillaris
ContRs0_13 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas_A Unclassified
ContRs0_14 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae Bosea Unclassified
ContRs0_15 Cont Rice straw 0 High-quality Bacteria Bacillota Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus lactis
ContRs0_16 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
ContRs0_18 Cont Rice straw 0 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Leucobacter Leucobacter sp020096995
ContRs0_19 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Nocardioidaceae Marmoricola Unclassified
ContRs0_2 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Pantoea Pantoea ananatis
ContRs0_20 Cont Rice straw 0 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Kineosporiaceae R-H-3 Unclassified
ContRs0_21 Cont Rice straw 0 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Acetobacterales Acetobacteraceae Belnapia Unclassified
ContRs0_22 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Aureimonas Aureimonas altamirensis
ContRs0_23 Cont Rice straw 0 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Herbiconiux Herbiconiux sp013113715
ContRs0_24 Cont Rice straw 0 Mid-quality Bacteria Bacillota Bacilli Lactobacillales Enterococcaceae Enterococcus_D Enterococcus_D innesii
ContRs0_25 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter soli
ContRs0_26 Cont Rice straw 0 High-quality Bacteria Bacillota Bacilli Bacillales Bacillaceae Bacillus Bacillus altitudinis
ContRs0_27 Cont Rice straw 0 High-quality Bacteria Bacillota Bacilli Lactobacillales Lactobacillaceae Leuconostoc Leuconostoc pseudomesenteroides
ContRs0_28 Cont Rice straw 0 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomataceae Siphonobacter Unclassified
ContRs0_29 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Cellulomonadaceae Cellulomonas Cellulomonas taurus
ContRs0_30 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhodobacterales Rhodobacteraceae Cereibacter_A Cereibacter_A sphaeroides
ContRs0_31 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Phycicoccus Phycicoccus jejuensis
ContRs0_33 Cont Rice straw 0 High-quality Bacteria Bacillota Bacilli Lactobacillales Enterococcaceae Enterococcus_G Enterococcus_G sulfureus
ContRs0_34 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Ochrobactrum_A Ochrobactrum_A pseudogrignonensis
ContRs0_36 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium Sphingobium sp913773715
ContRs0_4 Cont Rice straw 0 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Microbacterium Microbacterium sp003293595
ContRs0_5 Cont Rice straw 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium Methylobacterium sp900112625
ContRs0_9 Cont Rice straw 0 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium anyangense
ContRs1_10 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium kyogaense
ContRs1_11 Cont Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
ContRs1_12 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Leucobacter Leucobacter sp020096995
ContRs1_13 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Terracoccus Unclassified
ContRs1_14 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
ContRs1_15 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Unclassified Unclassified
ContRs1_16 Cont Rice straw 1 High-quality Bacteria Myxococcota Myxococcia Myxococcales Myxococcaceae Melittangium Melittangium primigenium
ContRs1_17 Cont Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Unclassified
ContRs1_19 Cont Rice straw 1 Mid-quality Bacteria Myxococcota Polyangia Nannocystales Nannocystaceae Nannocystis Unclassified
ContRs1_20 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas_I Unclassified
ContRs1_21 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Shinella Shinella sumterensis
ContRs1_22 Cont Rice straw 1 High-quality Bacteria Bacillota Bacilli Lactobacillales Enterococcaceae Enterococcus_D Enterococcus_D innesii
ContRs1_24 Cont Rice straw 1 High-quality Bacteria Bacillota Bacilli Bacillales Bacillaceae_H Priestia Priestia megaterium
ContRs1_25 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Corynebacterium Unclassified
ContRs1_26 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium Methylobacterium sp900112625
ContRs1_27 Cont Rice straw 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Ochrobactrum_A Ochrobactrum_A pseudogrignonensis
ContRs1_28 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Pseudorhodoferax Unclassified
ContRs1_30 Cont Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Microbacterium Unclassified
ContRs1_33 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium Unclassified
ContRs1_34 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermabacteraceae Brachybacterium Brachybacterium sp005490785
ContRs1_35 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Herbaspirillum Herbaspirillum huttiense
ContRs1_36 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas_A Pseudoxanthomonas_A winnipegensis
ContRs1_37 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas_E Pseudomonas_E monteilii
ContRs1_38 Cont Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Olivibacter Unclassified
ContRs1_39 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Pseudonocardia Pseudonocardia alni
ContRs1_4 Cont Rice straw 1 High-quality Bacteria Deinococcota Deinococci Deinococcales Trueperaceae Truepera Unclassified
ContRs1_40 Cont Rice straw 1 High-quality Bacteria Bacillota Bacilli Staphylococcales Staphylococcaceae Mammaliicoccus Mammaliicoccus sciuri
ContRs1_41 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium anyangense
ContRs1_5 Cont Rice straw 1 Mid-quality Bacteria Chloroflexota Chloroflexia Thermomicrobiales UBA6265 JACCYX01 Unclassified
ContRs1_6 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Rhodococcus Rhodococcus kroppenstedtii
ContRs1_7 Cont Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas_D Luteimonas_D abyssi
ContRs1_8 Cont Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Microbacterium Unclassified
ContRs1_9 Cont Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Pararcticibacter Unclassified
FBpRs1_1 FBa Rice straw 1 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas_E Pseudomonas_E monteilii
FBpRs1_12 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Marihabitans Marihabitans melonis
FBpRs1_13 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium kyogaense
FBpRs1_15 FBa Rice straw 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Neorhizobium Unclassified
FBpRs1_16 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas_D Luteimonas_D abyssi
FBpRs1_17 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Actinomycetospora Actinomycetospora corticicola
FBpRs1_18 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Xanthobacteraceae Rhodopseudomonas Unclassified
FBpRs1_19 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Hyphomicrobium_C Unclassified
FBpRs1_2 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermabacteraceae Brachybacterium Unclassified
FBpRs1_20 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomataceae Dyadobacter Unclassified
FBpRs1_21 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Flavobacteriales Flavobacteriaceae Flavobacterium Unclassified
FBpRs1_22 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Pseudonocardia Pseudonocardia alni
FBpRs1_24 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas Unclassified
FBpRs1_25 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Unclassified Unclassified
FBpRs1_26 FBa Rice straw 1 High-quality Bacteria Cyanobacteriota Cyanobacteriia Cyanobacteriales Microcoleaceae Planktothrix Unclassified
FBpRs1_28 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp943913195
FBpRs1_29 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium corticibacterium
FBpRs1_3 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Herbaspirillum Herbaspirillum huttiense
FBpRs1_30 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomataceae Siphonobacter Unclassified
FBpRs1_31 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas_I Unclassified
FBpRs1_32 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Phycicoccus Phycicoccus jejuensis
FBpRs1_33 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Agrococcus Agrococcus terreus
FBpRs1_34 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
FBpRs1_35 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium sp001586775
FBpRs1_36 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Actinosynnema Actinosynnema auranticum
FBpRs1_38 FBa Rice straw 1 Mid-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium phlebotomi
FBpRs1_39 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria UBA7879 UBA5542 Unclassified Unclassified
FBpRs1_4 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Leucobacter Leucobacter sp020096995
FBpRs1_40 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Brevibacteriaceae Brevibacterium Brevibacterium sediminis
FBpRs1_41 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Beutenbergiaceae Pseudactinotalea Unclassified
FBpRs1_42 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Streptomycetales Streptomycetaceae Streptomyces Streptomyces bacillaris
FBpRs1_43 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium Methylobacterium sp900112625
FBpRs1_44 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methylopilaceae Unclassified Unclassified
FBpRs1_45 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudorhodoplanes Unclassified
FBpRs1_46 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Nocardioidaceae Marmoricola Unclassified
FBpRs1_47 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Microbacterium Unclassified
FBpRs1_48 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Microlunatus Unclassified
FBpRs1_49 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Nakamurellaceae Nakamurella Nakamurella flava
FBpRs1_5 FBa Rice straw 1 High-quality Bacteria Gemmatimonadota Gemmatimonadetes Longimicrobiales Longimicrobiaceae Longimicrobium Unclassified
FBpRs1_50 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
FBpRs1_51 FBa Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Kineosporiaceae R-H-3 Unclassified
FBpRs1_52 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium anyangense
FBpRs1_53 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria CAIQBE01 CAIQBE01 Unclassified Unclassified
FBpRs1_54 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas_I Unclassified
FBpRs1_55 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Microbacterium Microbacterium sp003293595
FBpRs1_56 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Terracoccus Unclassified
FBpRs1_57 FBa Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium arupense
FBpRs1_6 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium sp002500745
FBpRs1_7 FBa Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Cyclobacteriaceae Algoriphagus Unclassified
FBpRs1_8 FBa Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Ochrobactrum_A Ochrobactrum_A pseudogrignonensis
FBpNitRs1_10 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Patulibacter Unclassified
FBpNitRs1_11 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium sp002500745
FBpNitRs1_12 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Rhodothermia Rhodothermales Rubricoccaceae Unclassified Unclassified
FBpNitRs1_13 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas Unclassified
FBpNitRs1_14 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Nakamurellaceae Nakamurella Unclassified
FBpNitRs1_15 FBaNit Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
FBpNitRs1_16 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Pseudonocardia Pseudonocardia alni
FBpNitRs1_17 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Aureimonas Aureimonas altamirensis
FBpNitRs1_18 FBaNit Rice straw 1 Mid-quality Bacteria Chloroflexota Chloroflexia Thermomicrobiales UBA6265 CADCWK01 Unclassified
FBpNitRs1_19 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhodobacterales Rhodobacteraceae Paracoccus Paracoccus marcusii
FBpNitRs1_2 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Streptosporangiales Streptosporangiaceae Nocardiopsis Unclassified
FBpNitRs1_20 FBaNit Rice straw 1 High-quality Bacteria Deinococcota Deinococci Deinococcales Trueperaceae Truepera Unclassified
FBpNitRs1_21 FBaNit Rice straw 1 Mid-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium griseoflavum
FBpNitRs1_22 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium Methylobacterium sp900112625
FBpNitRs1_23 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Cellvibrionaceae UBA5868 Unclassified
FBpNitRs1_24 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Avipropionibacterium Unclassified
FBpNitRs1_25 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhodobacterales Rhodobacteraceae Amaricoccus Unclassified
FBpNitRs1_26 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Micrococcaceae Nesterenkonia Nesterenkonia stercoripullorum
FBpNitRs1_27 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Micromonosporaceae Micromonospora Micromonospora wenchangensis
FBpNitRs1_28 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Cellulomonadaceae Cellulomonas Cellulomonas taurus
FBpNitRs1_29 FBaNit Rice straw 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Unclassified
FBpNitRs1_30 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomataceae Spirosoma Unclassified
FBpNitRs1_31 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Marihabitans Marihabitans melonis
FBpNitRs1_32 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Leucobacter Leucobacter sp020096995
FBpNitRs1_33 FBaNit Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Unclassified Unclassified
FBpNitRs1_34 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Quadrisphaeraceae Pseudokineococcus Pseudokineococcus lusitanus
FBpNitRs1_35 FBaNit Rice straw 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Shinella Shinella sumterensis
FBpNitRs1_36 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Streptomycetales Streptomycetaceae Streptomyces Streptomyces olivaceus
FBpNitRs1_37 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium kyogaense
FBpNitRs1_38 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Streptosporangiales Streptosporangiaceae Nocardiopsis Nocardiopsis flavescens
FBpNitRs1_39 FBaNit Rice straw 1 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Unclassified Unclassified
FBpNitRs1_40 FBaNit Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Ochrobactrum_A Ochrobactrum_A pseudogrignonensis
FBpNitRs1_41 FBaNit Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Agrococcus Agrococcus terreus
FBpNitRs1_42 FBaNit Rice straw 1 High-quality Bacteria Armatimonadota Fimbriimonadia Fimbriimonadales Fimbriimonadaceae Fimbriimonas Unclassified
FBpNitRs1_43 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Nocardioidaceae Aeromicrobium Unclassified
FBpNitRs1_44 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Beutenbergiaceae CALKWS01 Unclassified
FBpNitRs1_45 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Microlunatus Unclassified
FBpNitRs1_46 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Olivibacter Unclassified
FBpNitRs1_48 FBaNit Rice straw 1 High-quality Bacteria Bacillota Bacilli Staphylococcales Staphylococcaceae Mammaliicoccus Mammaliicoccus sciuri
FBpNitRs1_49 FBaNit Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Terracoccus Unclassified
FBpNitRs1_5 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Kapaibacteriia OLB7 OLB7 JAFDZV01 Unclassified
FBpNitRs1_7 FBaNit Rice straw 1 High-quality Bacteria Chloroflexota Chloroflexia Chloroflexales Kallotenuaceae JACDGP01 Unclassified
FBpNitRs1_9 FBaNit Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Flavobacteriales Flavobacteriaceae Flavobacterium Unclassified
FCentRs1_1 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Agrobacterium Agrobacterium tumefaciens_B
FCentRs1_10 FCent Rice straw 1 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter pittii
FCentRs1_11 FCent Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niabella Unclassified
FCentRs1_12 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium kyogaense
FCentRs1_13 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Pseudonocardiaceae Pseudonocardia Pseudonocardia alni
FCentRs1_14 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhodobacterales Rhodobacteraceae Cereibacter_A Cereibacter_A johrii
FCentRs1_15 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Nakamurellaceae Nakamurella Unclassified
FCentRs1_16 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Aureimonas Aureimonas altamirensis
FCentRs1_17 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Beutenbergiaceae Pseudactinotalea Unclassified
FCentRs1_18 FCent Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomataceae Siphonobacter Unclassified
FCentRs1_19 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria CAIQBE01 CAIQBE01 Unclassified Unclassified
FCentRs1_2 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Leucobacter Leucobacter sp020096995
FCentRs1_20 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Aquincola Unclassified
FCentRs1_21 FCent Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Microbacteriaceae Agrococcus Agrococcus terreus
FCentRs1_22 FCent Rice straw 1 High-quality Bacteria Myxococcota Myxococcia Myxococcales Myxococcaceae Unclassified Unclassified
FCentRs1_23 FCent Rice straw 1 High-quality Bacteria Actinomycetota Acidimicrobiia Acidimicrobiales Iamiaceae Iamia Unclassified
FCentRs1_24 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Mycobacterium anyangense
FCentRs1_25 FCent Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium Unclassified
FCentRs1_26 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas_D Luteimonas_D abyssi
FCentRs1_27 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Nakamurellaceae Nakamurella Unclassified
FCentRs1_28 FCent Rice straw 1 Mid-quality Bacteria Gemmatimonadota Gemmatimonadetes Longimicrobiales Longimicrobiaceae Unclassified Unclassified
FCentRs1_29 FCent Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Dermatophilaceae Terracoccus Unclassified
FCentRs1_30 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Aliihoeflea Unclassified
FCentRs1_31 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Corynebacterium Unclassified
FCentRs1_32 FCent Rice straw 1 Mid-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Beutenbergiaceae Litorihabitans Unclassified
FCentRs1_34 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Cellvibrionaceae UBA5868 Unclassified
FCentRs1_35 FCent Rice straw 1 High-quality Bacteria Bacillota Bacilli Bacillales Bacillaceae Bacillus Bacillus altitudinis
FCentRs1_36 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Ochrobactrum_A Ochrobactrum_A pseudogrignonensis
FCentRs1_39 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Actinomycetales Brevibacteriaceae Brevibacterium Brevibacterium sediminis
FCentRs1_40 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Mycobacteriaceae Mycobacterium Unclassified
FCentRs1_41 FCent Rice straw 1 High-quality Bacteria Bacillota Bacilli Bacillales Bacillaceae_H Priestia Priestia megaterium
FCentRs1_42 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhodobacterales Rhodobacteraceae Paracoccus Paracoccus marcusii
FCentRs1_43 FCent Rice straw 1 High-quality Bacteria Actinomycetota Actinomycetes Propionibacteriales Propionibacteriaceae Unclassified Unclassified
FCentRs1_44 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Burkholderiaceae Herbaspirillum Herbaspirillum huttiense
FCentRs1_45 FCent Rice straw 1 High-quality Bacteria Bacillota Bacilli Staphylococcales Staphylococcaceae Mammaliicoccus Mammaliicoccus sciuri
FCentRs1_46 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Rhizobiaceae Aureimonas Aureimonas frigidaquae
FCentRs1_5 FCent Rice straw 1 High-quality Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Sphingobacterium Sphingobacterium sp002500745
FCentRs1_7 FCent Rice straw 1 High-quality Bacteria Cyanobacteriota Cyanobacteriia Cyanobacteriales Microcoleaceae Planktothrix Unclassified
FCentRs1_8 FCent Rice straw 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter sp013417555

GTDB taxonomy of soil MAGs

Bin Treatment Matrix Time MAG Domain Phylum Class Order Family Genus Species
ContSoil0_1 Cont ContSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
ContSoil0_11 Cont ContSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
ContSoil0_12 Cont ContSoil0 0 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
ContSoil0_14 Cont ContSoil0 0 High-quality Bacteria Pseudomonadota Gammaproteobacteria Burkholderiales Gallionellaceae Sideroxyarcus Unclassified
ContSoil0_15 Cont ContSoil0 0 Mid-quality Bacteria Desulfobacterota_E Deferrimicrobia Deferrimicrobiales Deferrimicrobiaceae FEB-35 Unclassified
ContSoil0_16 Cont ContSoil0 0 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
ContSoil0_2 Cont ContSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
ContSoil0_4 Cont ContSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
ContSoil0_5 Cont ContSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
ContSoil0_6 Cont ContSoil0 0 Mid-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
ContSoil0_7 Cont ContSoil0 0 Mid-quality Archaea Methanobacteriota Methanobacteria Methanobacteriales Methanobacteriaceae Methanobacterium_D Unclassified
ContSoil0_9 Cont ContSoil0 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
ContSoil1_1 Cont ContSoil1 1 Mid-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
ContSoil1_10 Cont ContSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
ContSoil1_12 Cont ContSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
ContSoil1_13 Cont ContSoil1 1 High-quality Bacteria Tectomicrobia Entotheonellia J063 Unclassified Unclassified Unclassified
ContSoil1_15 Cont ContSoil1 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Beijerinckiaceae JAIXTM01 Unclassified
ContSoil1_17 Cont ContSoil1 1 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
ContSoil1_19 Cont ContSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
ContSoil1_2 Cont ContSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
ContSoil1_3 Cont ContSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
ContSoil1_4 Cont ContSoil1 1 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
ContSoil1_5 Cont ContSoil1 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Steroidobacterales Steroidobacteraceae Unclassified Unclassified
ContSoil1_6 Cont ContSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 JACCXG01 Unclassified
ContSoil1_7 Cont ContSoil1 1 Mid-quality Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Unclassified Unclassified
FBpSoil0_1 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FBpSoil0_10 FBa FBpSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae TH1177 Unclassified
FBpSoil0_14 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FBpSoil0_15 FBa FBpSoil0 0 Mid-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpSoil0_16 FBa FBpSoil0 0 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpSoil0_18 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Gaiellales Gaiellaceae GMQP-bins7 Unclassified
FBpSoil0_19 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FBpSoil0_2 FBa FBpSoil0 0 Mid-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpSoil0_20 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FBpSoil0_21 FBa FBpSoil0 0 Mid-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Micromonosporaceae JAEZGP01 Unclassified
FBpSoil0_22 FBa FBpSoil0 0 Mid-quality Bacteria Tectomicrobia Entotheonellia J063 Unclassified Unclassified Unclassified
FBpSoil0_23 FBa FBpSoil0 0 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FBpSoil0_3 FBa FBpSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpSoil0_4 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpSoil0_5 FBa FBpSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FBpSoil0_6 FBa FBpSoil0 0 High-quality Bacteria Pseudomonadota Gammaproteobacteria Steroidobacterales Steroidobacteraceae Unclassified Unclassified
FBpSoil0_7 FBa FBpSoil0 0 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpSoil0_8 FBa FBpSoil0 0 High-quality Bacteria Patescibacteria Microgenomatia UBA10105 UBA927 UBA927 Unclassified
FBpSoil1_1 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FBpSoil1_10 FBa FBpSoil1 1 High-quality Bacteria Patescibacteria Microgenomatia UBA10105 UBA927 UBA927 Unclassified
FBpSoil1_12 FBa FBpSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpSoil1_13 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Gaiellales Gaiellaceae GMQP-bins7 Unclassified
FBpSoil1_14 FBa FBpSoil1 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FBpSoil1_17 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FBpSoil1_19 FBa FBpSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpSoil1_2 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpSoil1_20 FBa FBpSoil1 1 Mid-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpSoil1_21 FBa FBpSoil1 1 Mid-quality Bacteria Desulfobacterota_E Deferrimicrobia Deferrimicrobiales Deferrimicrobiaceae FEB-35 Unclassified
FBpSoil1_22 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FBpSoil1_23 FBa FBpSoil1 1 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpSoil1_3 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpSoil1_4 FBa FBpSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FBpSoil1_5 FBa FBpSoil1 1 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Steroidobacterales Steroidobacteraceae Unclassified Unclassified
FBpSoil1_9 FBa FBpSoil1 1 High-quality Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Unclassified Unclassified
FBpNitSoil0_1 FBaNit FBpNitSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpNitSoil0_10 FBaNit FBpNitSoil0 0 Mid-quality Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium Unclassified
FBpNitSoil0_12 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FBpNitSoil0_14 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota Acidimicrobiia Acidimicrobiales Ilumatobacteraceae Unclassified Unclassified
FBpNitSoil0_15 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FBpNitSoil0_17 FBaNit FBpNitSoil0 0 High-quality Bacteria Desulfobacterota_E Deferrimicrobia Deferrimicrobiales Deferrimicrobiaceae FEB-35 Unclassified
FBpNitSoil0_18 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpNitSoil0_2 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FBpNitSoil0_20 FBaNit FBpNitSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpNitSoil0_21 FBaNit FBpNitSoil0 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FBpNitSoil0_3 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpNitSoil0_7 FBaNit FBpNitSoil0 0 Mid-quality Bacteria Bacteroidota Bacteroidia Bacteroidales Prolixibacteraceae Draconibacterium Unclassified
FBpNitSoil0_8 FBaNit FBpNitSoil0 0 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FBpNitSoil1_1 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FBpNitSoil1_10 FBaNit FBpNitSoil1 1 High-quality Bacteria Pseudomonadota Gammaproteobacteria Steroidobacterales Steroidobacteraceae Unclassified Unclassified
FBpNitSoil1_11 FBaNit FBpNitSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpNitSoil1_13 FBaNit FBpNitSoil1 1 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FBpNitSoil1_14 FBaNit FBpNitSoil1 1 High-quality Bacteria Tectomicrobia Entotheonellia Entotheonellales Entotheonellaceae SXND01 Unclassified
FBpNitSoil1_15 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FBpNitSoil1_16 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Gaiellales Gaiellaceae GMQP-bins7 Unclassified
FBpNitSoil1_17 FBaNit FBpNitSoil1 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FBpNitSoil1_18 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FBpNitSoil1_19 FBaNit FBpNitSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FBpNitSoil1_20 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FBpNitSoil1_21 FBaNit FBpNitSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FBpNitSoil1_23 FBaNit FBpNitSoil1 1 High-quality Bacteria Acidobacteriota Blastocatellia RBC074 RBC074 JAJVID01 Unclassified
FBpNitSoil1_24 FBaNit FBpNitSoil1 1 High-quality Bacteria Chloroflexota Limnocylindria Limnocylindrales CSP1-4 UBA5189 Unclassified
FBpNitSoil1_4 FBaNit FBpNitSoil1 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Xanthobacteraceae VAZQ01 Unclassified
FBpNitSoil1_5 FBaNit FBpNitSoil1 1 High-quality Bacteria Patescibacteria Microgenomatia UBA10105 UBA927 UBA927 Unclassified
FBpNitSoil1_7 FBaNit FBpNitSoil1 1 Mid-quality Bacteria Gemmatimonadota Gemmatimonadetes Gemmatimonadales GWC2-71-9 SZUA-320 Unclassified
FCentSoil0_1 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FCentSoil0_10 FCent FCentSoil0 0 High-quality Bacteria Tectomicrobia Entotheonellia J063 Unclassified Unclassified Unclassified
FCentSoil0_11 FCent FCentSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FCentSoil0_14 FCent FCentSoil0 0 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FCentSoil0_15 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FCentSoil0_17 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Gaiellales Gaiellaceae GMQP-bins7 Unclassified
FCentSoil0_18 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FCentSoil0_19 FCent FCentSoil0 0 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FCentSoil0_2 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FCentSoil0_4 FCent FCentSoil0 0 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FCentSoil0_5 FCent FCentSoil0 0 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FCentSoil0_6 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FCentSoil0_9 FCent FCentSoil0 0 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FCentSoil1_1 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 HRBIN12 CALGFI01 Unclassified
FCentSoil1_10 FCent FCentSoil1 1 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae TH1177 Unclassified
FCentSoil1_11 FCent FCentSoil1 1 Mid-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FCentSoil1_12 FCent FCentSoil1 1 Mid-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales 70-9 Unclassified Unclassified
FCentSoil1_13 FCent FCentSoil1 1 Mid-quality Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium Unclassified
FCentSoil1_14 FCent FCentSoil1 1 High-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FCentSoil1_15 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota Acidimicrobiia UBA5794 ZC4RG35 JARDZU01 Unclassified
FCentSoil1_16 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Gaiellales Gaiellaceae GMQP-bins7 Unclassified
FCentSoil1_17 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota Actinomycetes Mycobacteriales Micromonosporaceae JAEZGP01 Unclassified
FCentSoil1_18 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota UBA4738 UBA4738 CALAEC01 CALAEC01 Unclassified
FCentSoil1_19 FCent FCentSoil1 1 High-quality Bacteria Actinomycetota Thermoleophilia Solirubrobacterales Thermoleophilaceae JACVRW01 Unclassified
FCentSoil1_2 FCent FCentSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FCentSoil1_21 FCent FCentSoil1 1 High-quality Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales 2-12-FULL-66-21 Unclassified Unclassified
FCentSoil1_23 FCent FCentSoil1 1 High-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FCentSoil1_24 FCent FCentSoil1 1 Mid-quality Archaea Thermoproteota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Unclassified
FCentSoil1_4 FCent FCentSoil1 1 Mid-quality Bacteria Pseudomonadota Alphaproteobacteria Rhizobiales Methyloligellaceae Methyloceanibacter Unclassified
FCentSoil1_5 FCent FCentSoil1 1 Mid-quality Bacteria Pseudomonadota Gammaproteobacteria Steroidobacterales Steroidobacteraceae Unclassified Unclassified
FCentSoil1_8 FCent FCentSoil1 1 High-quality Bacteria Patescibacteria Microgenomatia UBA10105 UBA927 UBA927 Unclassified
FCentSoil1_9 FCent FCentSoil1 1 Mid-quality Bacteria Acidobacteriota Thermoanaerobaculia UBA5066 Gp7-AA6 Gp7-AA6 Unclassified